He first entered local politics in 1979 when he won a seat on Kilkenny Borough Council and was a subsequent Mayor of the city from 1996 to 1997.[2] He was the third generation of his family to serve on this council. From 1991 until the abolition of the dual mandate in 2003, he was also member of Kilkenny County Council, where his father, Michael McGuinness, was the longest-serving councillor (1959–99).[3]

On 22 April 2009, as part of cost-cutting measures due to the Irish financial crisis, the TaoiseachBrian Cowen reduced the number of Ministers of State from 20 to 15. McGuinness was among the seven junior ministers who were not reappointed. On 24 April 2009, he criticised Coughlan and Cowen for their lack of leadership being given to the country. He said: "She's not equipped to deal with the complex issues of dealing with enterprise and business within the department. And neither is the department".[6][7] McGuinness' later rejected suggestions he campaigned to undermine Coughlan, when it was revealed that he had hired external PR advice in an effort to enhance his own profile as a Minister of State within the Department.[8]

In 2010, a political memoir that he co-wrote with Naoise Nunn, called The House Always Wins, was published by Gill & Macmillan.[9][10]

He is the Fianna Fáil spokesperson on Small Business and Regulatory Framework since April 2011.

McGuinness was appointed as Chair of the Finance, Public Expenditure and Reform, and Taoiseach Committee on 14 June 2016.